I don't know what the smoke situation is likely to be at the times you would be passing through the various areas, maybe someone else can comment on that.
When/where it is likely to be cold, I'd try to avoid camping at higher elevations, staying partway down the mountain.
I hate hot weather and had plenty of it on my TA. I think that fall on the TA would actually be nicer than a hot Summer tour there.
McKenzie Pass was mentioned... I agree that it is likely to be open unless there is an especially early closing this year, but if it were to close Santiam Pass is plowed year round and would be a fall back option.